Data from: Isolation by distance and isolation by environment contribute to population differentiation in Protea repens (Proteaceae L.), a widespread South African species

PREMISE OF THE STUDY: The Cape Floristic Region (CFR) of South Africa is renowned for its botanical diversity, but the evolutionary origins of this diversity remain controversial. Both neutral and adaptive processes have been implicated in driving diversification, but population-level studies of plants in the CFR are rare. Here, we investigate the limits to gene flow and potential environmental drivers of selection in Protea repens L. (Proteaceae L.), a widespread CFR species. METHODS: We sampled 19 populations across the range of P. repens and used genotyping by sequencing to identify 2066 polymorphic loci in 663 individuals. We used a Bayesian FST outlier analysis to identify single-nucleotide polymorphisms (SNPs) marking genomic regions that may be under selection; we used those SNPs to identify potential drivers of selection and excluded them from analyses of gene flow and genetic structure. RESULTS: A pattern of isolation by distance suggested limited gene flow between nearby populations. The populations of P. repens fell naturally into two or three groupings, which corresponded to an east-west split. Differences in rainfall seasonality contributed to diversification in highly divergent loci, as do barriers to gene flow that have been identified in other species. CONCLUSIONS: The strong pattern of isolation by distance is in contrast to the findings in the only other widespread species in the CFR that has been similarly studied, while the effects of rainfall seasonality are consistent with well-known patterns. Assessing the generality of these results will require investigations of other CFR species.

研究背景：南非开普植物区（Cape Floristic Region, CFR）以极高的植物多样性著称，但该区域物种多样性的进化起源仍颇具争议。中性演化与适应性演化过程均被认为推动了物种分化，但针对开普植物区植物的种群水平研究仍相对匮乏。本研究以广泛分布于开普植物区的匍匐帝王花Protea repens L.（山龙眼科Proteaceae L.）为研究对象，探讨其基因流限制因素与潜在的环境选择驱动因子。
研究方法：我们在匍匐帝王花的整个分布范围内共采集19个种群的样本，通过基于测序的基因分型（genotyping by sequencing）技术，在663个个体中鉴定出2066个多态性位点。我们采用贝叶斯FST异常值分析，识别出可能处于选择压力下的基因组区域对应的单核苷酸多态性（single-nucleotide polymorphisms, SNPs）；利用这些SNPs筛选潜在的选择驱动因子，并将其排除在基因流与遗传结构分析之外。
研究结果：距离隔离模式表明，邻近种群间的基因流受到限制。匍匐帝王花的种群可自然划分为2个或3个聚类群，其分布对应东西向的地理分化。降雨季节型的差异对高度分化位点的物种分化具有贡献，同时已在其他物种中被证实的基因流障碍也发挥了作用。
研究结论：本研究观测到的强烈距离隔离模式，与此前仅有的另一项针对开普植物区广布物种的同类研究结果相悖；而降雨季节型的影响则与已知的演化模式相符。要评估这些结果的普遍性，还需对开普植物区的其他物种开展相关研究。